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Sample GSM12884 Query DataSets for GSM12884
Status Public on Jan 18, 2004
Title Adult 8hr
Sample type RNA
 
Channel 1
Source name CF512 animals, adult age 8hr
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name Reference sample A2
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description We wished to study normal adult aging in C. elegans. We competitively hybridized a series of experimental samples (experimental variable: adult age) against a common reference sample.

We use the CF512 fer-15(b26) II; fem-1 (hc17) IV mutant strain, which has defective spermatids which fail to activate into spermatozoa at 25C. Culturing this strain at 25C prevented self-fertilization and therefore eliminated contributions from embryonic transcripts. CF512 animals develop an otherwise-normal germ line; their lifespan and aging are similar to wild-type animals.

We axenized eggs and then synchronized animals via L1 arrest. Populations were very tightly synchronized. Animals were cultured at 25C. Samples were extracted and hybridized as described in protocols at http://microarrays.org.
Keywords = aging
 
Submission date Nov 11, 2003
Last update date May 28, 2005
Contact name Coleen T Murphy
E-mail(s) cmurphy@worms.ucsf.edu
Phone 415-341-8864
Organization name University of California, San Francisco
Department Biochemistry Department
Lab Kenyon lab
Street address
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL576
Series (1)
GSE832 Adult aging in C. elegans

Data table header descriptions
ID_REF
VALUE Normalized, adjusted log-expression ratio
F635_Median median pixel intensity of feature for Cy5 channel - in this experiment Cy5 channel is normal whole brain (reference) throughout the data set
F635_Mean mean pixel intensity of feature for Cy5 channel
F635_SD Cy5 pixel intensity standard deviation
B635_Median median Cy5 feature background intensity
B635_Mean mean Cy5 feature background intensity
B635_SD Cy5 background pixel intensity standard deviation
Pct_exceeding_B635plus1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
Pct_exceeding_B635plus2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635_Pct_Sat percentage of pixel saturation within feature
F532_Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532_Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532_Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532_Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
Pct_exceeding_B532plus1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
Pct_exceeding_B532plus2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
F532_Pct_Sat percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio_of_Medians ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio_of_Means ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median_of_Ratios median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean_of_Ratios arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios_SD standard deviation of the log of pixel intensity ratios. Note: ratios greater than 100 and less than 0.01 are excluded when calculating this data type
Rgn_Correlationtio regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn_Correlation coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F_Pixels number of feature pixels
B_Pixels number of background pixels
Sum_of_Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum_of_Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Log_Ratio base two logarithm of the ratio of medians
F635_Median_minus_B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532_Median_minus_B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635_Mean_minus_B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532_Mean_minus_B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags sub-standard features will have a negative value, while a good feature will have a positive value

Data table
ID_REF VALUE F635_Median F635_Mean F635_SD B635_Median B635_Mean B635_SD Pct_exceeding_B635plus1SD Pct_exceeding_B635plus2SD F635_Pct_Sat F532_Median F532_Mean F532_SD B532_Median B532_Mean B532_SD Pct_exceeding_B532plus1SD Pct_exceeding_B532plus2SD F532_Pct_Sat Ratio_of_Medians Ratio_of_Means Median_of_Ratios Mean_of_Ratios Ratios_SD Rgn_Correlationtio Rgn_Correlation F_Pixels B_Pixels Sum_of_Medians Sum_of_Means Log_Ratio F635_Median_minus_B635 F532_Median_minus_B532 F635_Mean_minus_B635 F532_Mean_minus_B532 Flags
1.1.1 -0.252 1250 1163 704 165 173 80 88 81 0 1138 1128 686 288 309 288 71 63 0 1.276 1.188 1.241 1.393 0.658 0.823 0.690 156 668 1935 1838 0.352 1085 850 998 840 0
1.2.1 -0.255 3666 3940 3495 183 190 65 78 76 0 3057 3319 2779 321 346 278 69 65 0 1.273 1.253 1.270 1.956 5.838 1.226 0.966 156 621 6219 6755 0.348 3483 2736 3757 2998 0
1.3.1 1.398 668 720 561 196 217 116 64 58 0 470 686 532 352 379 121 49 41 0 4.000 1.569 1.516 3.338 4.780 1.004 0.735 156 621 590 858 2.000 472 118 524 334 0
1.4.1 0.156 7919 6961 5484 176 193 110 82 77 0 4921 4380 3242 345 365 106 80 75 0 1.692 1.682 1.689 1.837 1.737 1.672 0.984 156 603 12319 10820 0.759 7743 4576 6785 4035 0
1.5.1 -0.036 2183 2635 2510 162 175 120 76 70 0 1698 2171 1903 334 344 80 74 71 0 1.482 1.346 1.343 1.695 1.718 1.312 0.975 156 652 3385 4310 0.567 2021 1364 2473 1837 0
1.6.1 -0.482 664 730 514 166 180 119 71 62 0 782 848 479 324 331 73 71 66 0 1.087 1.076 1.077 1.275 0.954 1.009 0.889 156 675 956 1088 0.121 498 458 564 524 0
1.7.1 0.175 15992 13476 10687 173 181 61 92 90 0 9529 8387 6600 307 314 63 89 85 0 1.715 1.646 1.634 1.900 1.258 1.627 0.990 156 666 25041 21383 0.779 15819 9222 13303 8080 0
1.8.1 0.018 2665 2531 2046 174 184 69 83 77 0 1925 1947 1448 305 315 80 77 71 0 1.538 1.435 1.425 1.628 1.135 1.403 0.972 156 654 4111 3999 0.621 2491 1620 2357 1642 0
1.9.1 -0.221 30069 23193 16131 173 185 102 89 87 0 23247 18440 12692 303 312 79 88 83 0 1.303 1.269 1.275 1.436 0.816 1.265 0.992 156 652 52840 41157 0.382 29896 22944 23020 18137 0
1.10.1 0.172 33353 28567 15037 179 189 103 100 100 0 19685 16618 7789 297 307 79 99 98 0 1.711 1.739 1.753 1.851 0.922 1.775 0.984 156 627 52562 44709 0.775 33174 19388 28388 16321 0
1.11.1 -0.345 3955 3512 2807 182 186 53 82 75 0 3446 2892 2168 292 300 65 77 72 0 1.196 1.281 1.262 1.374 0.811 1.270 0.976 156 659 6927 5930 0.259 3773 3154 3330 2600 0
1.12.1 -0.182 3249 3126 2589 180 186 64 75 71 0 2590 2399 1878 299 304 56 75 71 0 1.340 1.403 1.376 1.733 2.095 1.367 0.969 156 650 5360 5046 0.422 3069 2291 2946 2100 0
1.13.1 -0.122 10228 8690 7205 181 197 109 78 75 0 7504 6545 5245 306 310 71 82 79 0 1.396 1.364 1.361 1.450 1.129 1.359 0.986 156 644 17245 14748 0.481 10047 7198 8509 6239 0
1.14.1 0.215 8352 8767 7378 184 198 84 79 76 0 4942 5201 4225 309 324 114 76 74 0 1.763 1.754 1.765 2.141 3.089 1.738 0.987 156 663 12801 13475 0.818 8168 4633 8583 4892 0
1.15.1 -0.269 1285 1430 1144 182 197 86 73 69 0 1183 1288 876 308 324 117 75 66 0 1.261 1.273 1.222 1.383 1.351 1.256 0.952 156 675 1978 2228 0.334 1103 875 1248 980 0
1.16.1 0.002 8074 7150 5475 182 189 67 83 78 0 5491 4780 3426 302 308 74 83 80 0 1.521 1.556 1.513 1.534 1.007 1.568 0.987 156 689 13081 11446 0.605 7892 5189 6968 4478 0
1.17.1 -0.185 5448 4820 3785 175 184 61 81 76 0 4247 3705 2763 301 332 697 66 63 0 1.336 1.365 1.353 1.373 0.652 1.357 0.982 156 667 9219 8049 0.418 5273 3946 4645 3404 0
1.18.1 -0.371 1274 1280 959 174 182 58 78 72 0 1232 1194 763 296 331 714 59 28 0 1.175 1.232 1.189 1.389 1.259 1.000 0.776 156 636 2036 2004 0.233 1100 936 1106 898 0
1.19.1 -0.490 744 797 574 177 186 78 69 62 0 823 852 505 299 309 77 70 62 0 1.082 1.121 1.085 1.206 0.929 1.082 0.924 156 603 1091 1173 0.114 567 524 620 553 0
1.20.1 0.017 2656 2352 1620 177 183 61 89 85 0 1906 1831 1153 293 302 70 87 83 0 1.537 1.414 1.424 1.452 0.579 1.393 0.966 156 608 4092 3713 0.620 2479 1613 2175 1538 0

Total number of rows: 20000

Table truncated, full table size 3217 Kbytes.




Supplementary data files not provided
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